ChimeraX Recipes

Select overlapping atoms

Here is Python code defining a command “overlapped” that selects atoms that are on top of other atoms. I was trying to make an iron-oxide crystal hematite from the unit cell and it produced many atoms exactly on top of each other. The overlapped command let me select and delete the duplicate atoms. The first copy of an atom at a position is not selected, but all other copies within 0.1 Angstroms are selected (use “distance” option to change tolerance). Open the Python code to define the command


then use the command to select and remove the duplicate atoms from the crystal with asymmetric unit hematite_asym_unit.cif.

open hematite_asym_unit.cif
unitcell #1 cells 3,3,1
combine #2 name hematite_crystal
overlap #3
delete sel

This doesn’t create the correct bonds for the crystal. We can add the bonds with the connect command and save the result hematite_crystal.mol2.

~bond #3
connect #3
save hematite_crystal.mol2 model #3

Here is the code:

# Select atoms that overlap previous atoms within a specified distance.
# Opening this Python defines the "overlapped" command.  Example use
#        overlap #1 distance 0.3

def overlapped_atoms(session, atoms, distance = 0.1):
    xyz = atoms.scene_coords
    from numpy import zeros
    dup = zeros((len(atoms),), bool)
    from chimerax.geometry import find_close_points
    for i,a in enumerate(atoms):
        if not dup[i]:
            i1, i2 = find_close_points([a.scene_coord], xyz, distance)
            dup[i2] = True
            dup[i] = False
    datoms = atoms[dup]
    datoms.selected = True
    n = len(datoms)
    session.logger.status(f'{n} overlapped atoms', log=True)
    return datoms

def register_command(logger):
    from chimerax.core.commands import register, CmdDesc, FloatArg
    from chimerax.atomic import AtomsArg
    desc = CmdDesc(required = [('atoms', AtomsArg)],
                   keyword = [('distance', FloatArg)],
                   synopsis='Select overlapped atoms')
    register('overlapped', desc, overlapped_atoms, logger=logger)


Tom Goddard, March 16, 2022